This is a technical issue for me

When setting up my game I have this to setup outside my game so everything defaults to it. Do I need to add script for what I want for bar 1, bar2 and bar 3 ? i.e. health , magic points and sanity for their specific script codes so when I make npcs or my players get their tokens right they don't have to go into the drop down menu and hunt for each ability ? If so, do I go into the game and copy the string of commands that represent each of the functions I want then on the game page paste them in the bars and save so I won't ever have to do that again for any NPCs or monsters ? 

Which Character sheet are you using? For PCs this is not an issue, just get them set up from the start.  For NPCs, if you are using a free Compendium resource such as the 5e SRD then yes, you would need an API script to auto-set them up.  If using a paid Compendium resource such as the 5e Monster Manual then you can use the campaign settings and that will be applied every time you pull from the Compendium.  For NPCs you do NOT want to set the Attribute. Just put the HP values into the Bar.  This is because when you link the bars it will change the value on the character sheet when the bar changes, and that will change it for ALL instances of that creature.  Example 1: If the Goblin token has HP on the health bar Attribute then when you change one Goblin's HP it will change all Goblin's HP.  Example 2: If the goblin token has None on the health bar Attribute but has the boxes filled out with numbers then when you change one Goblins Health it will only change that Goblins health. 

Call of Cthulhu character 7th ed sheet. I fiddle with it and I see hat you mean. On one hand I don't want them to be mooks incase we end abruptly and we have a chance of losing the data- on the other hand if it sees 1 mob as all for its health I'm kinda hosed. Can I do a copy and paste and rename the mob like thug 1-4 and it will keep or because they will all share the same sheet I still can't get around it and I just have to make 4 seperate sheets. 

The data will not get lost, the tokens will keep the health data. The character sheets are not required for health.  Standard setup is to use one character sheet per NPC, then have the tokens each have their separate (not linked to the character sheet) health bars. There is no data loss issue. 

I just make sure to save and update after I fill in the NPC and itll keep ?

Ok, to clarify here you are talking about two different things.  A) Setting up a token, this is where saving and updating comes into play.  B) Using the health bars of a token, this is where the 'no data loss' statement comes into play.  Set up the token properly, including setting it as the default token on the character. You can do this from the token settings or from the Character's edit.  1. Set the represents to the NPC character sheet. Set/change name as needed, click the 3 dots to set up who can see the name.  2. Set the values for health, do NOT set the Attribute. Click the 3 dots to set up who can see the bar, numbers, etc.  3. Set the Attribute for other things, like AC. Again, click the 3 dots to set up who can see the bar, numbers, etc. NOTE: if the attribute functions like health, with every token having different values then use the setup for step #2.  4. Update the token to the Character. This can be done on the Token settings or via Use Selected Token on the Character (hit Edit). Note: If editing from the Character rather than the Token then step 4 shouldn't be necessary, but no harm to do it anyhow. 5. Save.  6. Optional: Apply Token Defaults sets up all tokens linked to the character with the new settings.    If you have any questions on the specifics of setting tokens feel free to ask.

In order for the dropdowns to show up the token needs to be linked to a character sheet as Gauss already mentioned... If this is done, you can set up the bars all you want and if you then link it (as mentioned by Gauss as well) it will be saved and whenever you drag the token out to the VTT you have the Bars set with their respective values... The Keeper said: When setting up my game I have this to setup outside my game so everything defaults to it. Do I need to add script for what I want for bar 1, bar2 and bar 3 ? i.e. health , magic points and sanity for their specific script codes so when I make npcs or my players get their tokens right they don't have to go into the drop down menu and hunt for each ability ? If so, do I go into the game and copy the string of commands that represent each of the functions I want then on the game page paste them in the bars and save so I won't ever have to do that again for any NPCs or monsters ? 

Can I ever have more than 3 bars up at a time ?

No, there’s only 3 bars. I’m using the Tooltip for defenses in my 13th Age games to speed play.